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- PDB-3zw9: CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE ... -

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Basic information

Entry
Database: PDB / ID: 3zw9
TitleCRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH (2S,3S)-3-HYDROXY-2-METHYLBUTANOYL-COA
ComponentsPEROXISOMAL BIFUNCTIONAL ENZYME
KeywordsOXIDOREDUCTASE / BETA OXIDATION PATHWAY / LIPID METABOLISM / LYASE / ISOMERASE / PEROXISOME / FATTY ACID METABOLISM
Function / homology
Function and homology information


Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity ...Beta-oxidation of very long chain fatty acids / intramolecular oxidoreductase activity, transposing C=C bonds / Peroxisomal protein import / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / peroxisome / enzyme binding / cytosol
Similarity search - Function
N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (2S,3S)-3-HYDROXY-2-METHYLBUTANOYL-COA / Peroxisomal bifunctional enzyme
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKasaragod, P. / Schmitz, W. / Hiltunen, J.K. / Wierenga, R.K.
Citation
Journal: FEBS J. / Year: 2013
Title: The Isomerase and Hydratase Reaction Mechanism of the Crotonase Active Site of the Multifunctional Enzyme (Type-1), as Deduced from Structures of Complexes with 3S-Hydroxy- Acyl-Coa.
Authors: Kasaragod, P. / Schmitz, W. / Kalervo Hiltunen, J. / Wierenga, R.K.
#1: Journal: J.Biol.Chem. / Year: 2010
Title: The Crystal Structure of Liganded Rat Peroxisomal Multifunctional Enzyme Type 1: A Flexible Molecule with Two Interconnected Active Sites
Authors: Kasaragod, P. / Venkatesan, R. / Kiema, T.R. / Hiltunen, J.K. / Wierenga, R.K.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXISOMAL BIFUNCTIONAL ENZYME
B: PEROXISOMAL BIFUNCTIONAL ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,2059
Polymers161,8632
Non-polymers3,3427
Water2,054114
1
A: PEROXISOMAL BIFUNCTIONAL ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5544
Polymers80,9311
Non-polymers1,6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEROXISOMAL BIFUNCTIONAL ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6515
Polymers80,9311
Non-polymers1,7194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.592, 126.652, 225.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAAA1 - 6121 - 81
21METMETALAALABB1 - 6121 - 81
12LEULEULEULEUAA75 - 25895 - 278
22LEULEULEULEUBB75 - 25895 - 278
13TRPTRPALAALAAA288 - 350308 - 370
23TRPTRPALAALABB288 - 350308 - 370
14LYSLYSGLYGLYAA361 - 473381 - 493
24LYSLYSGLYGLYBB361 - 473381 - 493
15GLYGLYHISHISAA477 - 718497 - 738
25GLYGLYHISHISBB477 - 718497 - 738

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein PEROXISOMAL BIFUNCTIONAL ENZYME / PBE / PBFE / MULTIFUNCTIONAL ENZYME TYPE-1 / ENOYL-COA HYDRATASE/3 / 2-TRANS-ENOYL-COA ISOMERASE / ...PBE / PBFE / MULTIFUNCTIONAL ENZYME TYPE-1 / ENOYL-COA HYDRATASE/3 / 2-TRANS-ENOYL-COA ISOMERASE / 3-HYDROXYACYL-COA DEHYDROGENASE


Mass: 80931.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Organ: PEROXISOME / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07896, enoyl-CoA hydratase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-T1G / (2S,3S)-3-HYDROXY-2-METHYLBUTANOYL-COA


Mass: 863.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H40N7O18P3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55.7 % / Description: NONE
Crystal growpH: 6
Details: 100MM MES PH 6.0, 150MM AMMONIUM SULPHATE, 15% W/V PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.15
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.9→49.5 Å / Num. obs: 42965 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 2.9→2.975 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→100 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.868 / SU B: 18.885 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28745 2147 5 %RANDOM
Rwork0.22781 ---
obs0.23076 40409 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.096 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11068 0 213 114 11395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.99915685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03651440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73723.304451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.949151934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6021578
X-RAY DIFFRACTIONr_chiral_restr0.1220.21740
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.57178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.285211556
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78134374
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2784.54129
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A244tight positional0.040.05
12B244tight positional0.040.05
21A736tight positional0.060.05
22B736tight positional0.060.05
31A252tight positional0.040.05
32B252tight positional0.040.05
41A452tight positional0.040.05
42B452tight positional0.040.05
51A968tight positional0.060.05
52B968tight positional0.060.05
11A204medium positional0.070.5
12B204medium positional0.070.5
21A665medium positional0.080.5
22B665medium positional0.080.5
31A203medium positional0.050.5
32B203medium positional0.050.5
41A402medium positional0.060.5
42B402medium positional0.060.5
51A974medium positional0.070.5
52B974medium positional0.070.5
11A244tight thermal0.210.5
12B244tight thermal0.210.5
21A736tight thermal0.20.5
22B736tight thermal0.20.5
31A252tight thermal0.080.5
32B252tight thermal0.080.5
41A452tight thermal0.10.5
42B452tight thermal0.10.5
51A968tight thermal0.150.5
52B968tight thermal0.150.5
11A204medium thermal0.242
12B204medium thermal0.242
21A665medium thermal0.192
22B665medium thermal0.192
31A203medium thermal0.082
32B203medium thermal0.082
41A402medium thermal0.112
42B402medium thermal0.112
51A974medium thermal0.162
52B974medium thermal0.162
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 169 -
Rwork0.334 2932 -
obs--100 %

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